i NEVER pre-wash my flannels more than once, i've used flannel in peiced tops and for backs on probably a hundred quilts...have NEVER had any problems with shrinkage after the quilt is made. the batting and the density of quilting also dictates how much a quilt will shrink...regardless of the fiber content of the top/back. i kind of feel like some people worry way too much about silly things.
that being said...if you purchase, single sided, thin flannel it may shrink more than a quality flannel